Feature Deep Dive: Open in App

BoehriT 
We had this very issue on our tenant. 

We had a meeting with the OneDrive team here recently who recommended hiding the button from all sites on our tenant using a cmdlet.

Connect-SPOService -Url https://contoso-admin.sharepoint.com    (change Url to your own tenant)

Set-SPOTenant -HideSyncButtonOnTeamSite $true

OR

Set-PnPTenant -HideSyncButtonOnTeamSite $true

Whether you use Set-SPOTenant or Set-PnPTenant depends on the version of PowerShell you use (I believe PnP is PowerShell 7).

Following running this script, the Sync buttons were hidden across all sites and I was still able to Open Documents in App (e.g., PDFs in Adobe) on those sites.

(Note Offline Availability is turned on in these sites, but the ability to sync has been removed for the user). 

Hopefully this helps some.